GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Pontibacillus litoralis JSM 072002

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_036834050.1 N784_RS08285 butyryl-CoA dehydrogenase

Query= BRENDA::Q96329
         (436 letters)



>NCBI__GCF_000775615.1:WP_036834050.1
          Length = 400

 Score =  174 bits (440), Expect = 6e-48
 Identities = 119/377 (31%), Positives = 186/377 (49%), Gaps = 5/377 (1%)

Query: 58  EEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSIKG-YGCPGLSIT 116
           E+Q +RK VRE ++KE+ P M E+ E+  F   I  KL  +G+ G  I   YG  G+   
Sbjct: 8   EQQMLRKTVREFVDKEIIPYMKEWDERGTFDPAIMHKLADLGLMGVCIPTKYGGSGMDYN 67

Query: 117 ANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWALTE 176
           A AI   E+ R D +  T + VH+ L  L++   G+E QKEKYL   A+   +  + LTE
Sbjct: 68  ALAIVCEELERGDTAFRTAVSVHTGLNSLSLLQFGTEEQKEKYLIPQAKGEKIGAFGLTE 127

Query: 177 PDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFA---RNTTTNQINGFIVK 233
           P  GSD + + TTAT+    + +NGQK WI     AD  ++FA   +      I+ FIV+
Sbjct: 128 PGAGSDVASIQTTATRKGDYYTLNGQKSWISLCDSADHFLVFAYTDKEKKHQGISAFIVE 187

Query: 234 KDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRL-PGVNSFQDTSKVLAVSRVMVA 292
           +   G  +     K+G+R    G++ L++V VP ++RL    + F+     L   R  VA
Sbjct: 188 RTMEGFSSKATKGKLGIRAGNTGELFLEDVPVPVDNRLGEEGDGFKIAMASLDNGRFTVA 247

Query: 293 WQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRLCKLYE 352
               G+ M   +   RY  ER+ FG  +   QL QQ +  M   +Q   L+ +R  +L  
Sbjct: 248 AGACGLMMACLEASVRYCHERETFGKEIGKHQLVQQMIANMEAGLQMSRLLVYRAGELKN 307

Query: 353 TGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYTYEGTYD 412
           +G+    + SL K      A + A    ++ G  G   ++ V +   + +    YEGT +
Sbjct: 308 SGKRNTRETSLAKWQACDFANKAADDAVQIHGAYGYSNEYAVERYLRNSKAPVIYEGTRE 367

Query: 413 INTLVTGREVTGIASFK 429
           I+T++    V G  + K
Sbjct: 368 IHTIMQAEYVLGYRTDK 384


Lambda     K      H
   0.319    0.133    0.399 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 349
Number of extensions: 17
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 436
Length of database: 400
Length adjustment: 32
Effective length of query: 404
Effective length of database: 368
Effective search space:   148672
Effective search space used:   148672
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory